[Biojava-dev] Biojava Interface to BLAST web/remote services

[Scooter Willis]

Sylvain

Given that BioJava already has a BLAST file parser that returns results
the goal should be to have a remote/web call return the same set of
classes as if you had parsed the file locally. That is going to be my
approach. Once we get a couple services working we can integrate into a
common factory/interface approach.

Thanks

Scooter


-----Original Message-----
From: biojava-dev-bounces at lists.open-bio.org
[mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of Sylvain
Foisy
Sent: Thursday, June 04, 2009 9:07 AM
To: Scooter Willis; Andreas Prlic
Cc: biojava-dev at lists.open-bio.org
Subject: Re: [Biojava-dev] Biojava Interface to BLAST web/remote
services

Hi Scooter,

On 04/06/09 07:38, "[NAME]" <[ADDRESS]> wrote:

> Looks like the rolled their own URL interface and did not do a WSDL.
Not a big
> deal but does appear they have some sort of submit get a "ticket" and
then
> check back with the "ticket" identifier for the results. The BioJava
API would
> hide the transport layer so you could use a custom URL approach or web
> services. 

That is basically the way it works. I am working on a RemoteBlastWrapper
class that would do exactly what you are writing.

  
> Not sure how the other WSDL interfaces handle long running tasks but I
assume
> the Web Services can handle a call that takes say 5 minutes to respond
without
> timing out. Some process would need to distinguish between a long
running
> server task and a server that is no longer responding.

We'll have to try ;-)

Best regards

Sylvain


===================================================================

 Sylvain Foisy, Ph. D.
 Consultant Bio-informatique / Bioinformatics
 Diploide.net - TI pour la vie / IT for Life

 Courriel: sylvain.foisy at diploide.net
 Web: http://www.diploide.net
 Tel: (514) 893-4363
===================================================================


_______________________________________________
biojava-dev mailing list
biojava-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-dev